I think with the headliner removed, you'll see where it makes sense to cut.

The tubes are just 1/2" clear plastic tubing that's stuffed down the A and C pillars to drain locations in the front fenders and rear quarters.

Nothing different about pillars on sunroof cars and non-sunroof.

I would not cut pillars, ever, unless I'm junking the car, or building a convertible. There are many layers of steel there, and you are messing with the windshield frame dimensions.

Good luck with this job, it's doable though not the simplest thing you could choose.

--Rob